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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        This report was generated using MultiQC, version 1.19

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-06-28, 02:32 EDT based on data in: /gpfs/radev/scratch/mcdougal/hl993/Cave/clean/fastqc_results


        General Statistics

        Showing 482/482 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        ERR10036468_1
        59.6%
        46%
        140 bp
        70.4
        ERR10036468_2
        53.8%
        45%
        140 bp
        70.4
        ERR10036469_1
        71.6%
        48%
        140 bp
        145.0
        ERR10036469_2
        63.9%
        48%
        140 bp
        145.0
        ERR10114878_1
        3.8%
        62%
        74 bp
        16.0
        ERR10114878_2
        3.8%
        62%
        74 bp
        16.0
        ERR10114879_1
        3.4%
        60%
        71 bp
        19.2
        ERR10114879_2
        3.4%
        60%
        71 bp
        19.2
        ERR10114880_1
        2.1%
        61%
        70 bp
        13.6
        ERR10114880_2
        2.1%
        61%
        70 bp
        13.6
        ERR10114881_1
        0.5%
        59%
        61 bp
        2.0
        ERR10114881_2
        0.5%
        59%
        61 bp
        2.0
        ERR10114882_1
        2.4%
        58%
        70 bp
        14.4
        ERR10114882_2
        2.3%
        58%
        70 bp
        14.4
        ERR10114883_1
        2.0%
        57%
        72 bp
        17.7
        ERR10114883_2
        2.0%
        57%
        72 bp
        17.7
        ERR10479404_1
        19.2%
        53%
        132 bp
        241.8
        ERR10479404_2
        17.9%
        53%
        132 bp
        241.8
        ERR1198911_1
        0.5%
        54%
        222 bp
        1.2
        ERR1198911_2
        0.6%
        54%
        222 bp
        1.2
        ERR1198912_1
        0.4%
        56%
        222 bp
        0.5
        ERR1198912_2
        0.3%
        56%
        222 bp
        0.5
        ERR1198913_1
        0.7%
        55%
        222 bp
        0.5
        ERR1198913_2
        0.6%
        55%
        222 bp
        0.5
        ERR1198914_1
        0.6%
        55%
        222 bp
        0.4
        ERR1198914_2
        0.5%
        55%
        222 bp
        0.4
        ERR1514431_1
        0.3%
        64%
        122 bp
        5.7
        ERR1514431_2
        0.3%
        64%
        122 bp
        5.7
        ERR1514432_1
        0.5%
        65%
        122 bp
        6.1
        ERR1514432_2
        0.5%
        65%
        122 bp
        6.1
        ERR1514433_1
        0.5%
        64%
        122 bp
        6.2
        ERR1514433_2
        0.5%
        64%
        122 bp
        6.2
        SRR10270686_1
        46.0%
        65%
        132 bp
        90.6
        SRR10270686_2
        46.3%
        65%
        132 bp
        90.6
        SRR11450778_1
        4.0%
        65%
        126 bp
        2.1
        SRR11450778_2
        3.9%
        65%
        126 bp
        2.1
        SRR12120648_1
        2.3%
        58%
        132 bp
        49.3
        SRR12120648_2
        2.3%
        58%
        132 bp
        49.3
        SRR12120649_1
        9.1%
        65%
        132 bp
        3.1
        SRR12120649_2
        9.1%
        65%
        132 bp
        3.1
        SRR12120650_1
        16.3%
        63%
        132 bp
        48.4
        SRR12120650_2
        16.3%
        63%
        132 bp
        48.4
        SRR12929264_1
        14.9%
        52%
        128 bp
        0.1
        SRR12929264_2
        15.2%
        52%
        128 bp
        0.1
        SRR12929265_1
        3.9%
        52%
        126 bp
        1.1
        SRR12929265_2
        3.9%
        52%
        126 bp
        1.1
        SRR12929266_1
        0.7%
        54%
        128 bp
        0.0
        SRR12929266_2
        0.7%
        54%
        126 bp
        0.0
        SRR12929267_1
        4.1%
        48%
        126 bp
        0.5
        SRR12929267_2
        4.2%
        48%
        126 bp
        0.5
        SRR12929268_1
        9.8%
        44%
        128 bp
        0.4
        SRR12929268_2
        9.9%
        44%
        128 bp
        0.4
        SRR12929269_1
        14.2%
        46%
        126 bp
        0.6
        SRR12929269_2
        14.2%
        46%
        126 bp
        0.6
        SRR12929270_1
        22.8%
        52%
        116 bp
        0.1
        SRR12929270_2
        23.4%
        52%
        116 bp
        0.1
        SRR14962752_1
        5.4%
        64%
        132 bp
        36.1
        SRR14962752_2
        5.4%
        64%
        132 bp
        36.1
        SRR14962753_1
        4.5%
        64%
        132 bp
        30.6
        SRR14962753_2
        4.5%
        64%
        132 bp
        30.6
        SRR14962754_1
        2.7%
        64%
        132 bp
        35.4
        SRR14962754_2
        2.8%
        64%
        132 bp
        35.4
        SRR14962755_1
        4.3%
        64%
        132 bp
        35.0
        SRR14962755_2
        4.4%
        64%
        132 bp
        35.0
        SRR14962756_1
        1.9%
        61%
        132 bp
        36.3
        SRR14962756_2
        2.0%
        61%
        132 bp
        36.3
        SRR1559028_1
        3.1%
        44%
        132 bp
        274.5
        SRR1559028_2
        2.9%
        44%
        132 bp
        274.5
        SRR1559230_1
        4.5%
        45%
        132 bp
        128.2
        SRR1559230_2
        4.5%
        45%
        130 bp
        128.2
        SRR1559353_1
        1.6%
        42%
        132 bp
        167.3
        SRR1559353_2
        1.6%
        42%
        132 bp
        167.3
        SRR1560064_1
        2.2%
        50%
        130 bp
        134.1
        SRR1560064_2
        2.3%
        50%
        132 bp
        134.1
        SRR1560266_1
        20.3%
        49%
        128 bp
        272.9
        SRR1560266_2
        19.6%
        49%
        130 bp
        272.9
        SRR1560848_1
        6.4%
        38%
        132 bp
        156.5
        SRR1560848_2
        6.5%
        38%
        132 bp
        156.5
        SRR1560849_1
        9.0%
        41%
        132 bp
        167.2
        SRR1560849_2
        8.8%
        41%
        132 bp
        167.2
        SRR1560850_1
        3.1%
        34%
        132 bp
        157.0
        SRR1560850_2
        3.1%
        34%
        132 bp
        157.0
        SRR16971103_1
        43.1%
        62%
        132 bp
        88.6
        SRR16971103_2
        41.2%
        62%
        132 bp
        88.6
        SRR16971104_1
        15.1%
        62%
        132 bp
        250.5
        SRR16971104_2
        14.3%
        62%
        132 bp
        250.5
        SRR16971105_1
        20.9%
        61%
        132 bp
        127.5
        SRR16971105_2
        20.0%
        61%
        132 bp
        127.5
        SRR16971106_1
        9.6%
        55%
        132 bp
        150.7
        SRR16971106_2
        9.3%
        55%
        132 bp
        150.7
        SRR16971107_1
        27.8%
        62%
        132 bp
        122.5
        SRR16971107_2
        26.8%
        62%
        132 bp
        122.5
        SRR16971108_1
        10.7%
        63%
        132 bp
        186.7
        SRR16971108_2
        10.3%
        63%
        132 bp
        186.7
        SRR16971109_1
        25.2%
        62%
        132 bp
        121.6
        SRR16971109_2
        24.2%
        62%
        132 bp
        121.6
        SRR18711753_1
        8.9%
        57%
        132 bp
        28.9
        SRR18711753_2
        8.7%
        57%
        132 bp
        28.9
        SRR19994649_1
        12.7%
        69%
        140 bp
        8.5
        SRR19994649_2
        12.4%
        69%
        140 bp
        8.5
        SRR19994650_1
        5.4%
        67%
        140 bp
        4.1
        SRR19994650_2
        5.5%
        67%
        140 bp
        4.1
        SRR19994651_1
        4.0%
        62%
        140 bp
        9.6
        SRR19994651_2
        3.7%
        62%
        140 bp
        9.6
        SRR22195396_1
        9.7%
        63%
        140 bp
        27.2
        SRR22195396_2
        9.3%
        63%
        140 bp
        27.2
        SRR22722176_1
        2.5%
        43%
        91 bp
        3.4
        SRR22722176_2
        2.5%
        43%
        91 bp
        3.4
        SRR22722177_1
        2.5%
        47%
        91 bp
        3.3
        SRR22722177_2
        2.5%
        47%
        91 bp
        3.3
        SRR22722178_1
        2.3%
        44%
        91 bp
        3.3
        SRR22722178_2
        2.2%
        44%
        91 bp
        3.3
        SRR22722179_1
        2.9%
        46%
        91 bp
        3.3
        SRR22722179_2
        2.7%
        45%
        91 bp
        3.3
        SRR22722180_1
        1.9%
        48%
        91 bp
        3.2
        SRR22722180_2
        1.8%
        48%
        91 bp
        3.2
        SRR22722181_1
        3.2%
        47%
        91 bp
        3.3
        SRR22722181_2
        3.3%
        47%
        91 bp
        3.3
        SRR22722182_1
        3.6%
        48%
        91 bp
        3.2
        SRR22722182_2
        3.5%
        48%
        91 bp
        3.2
        SRR22722183_1
        3.4%
        49%
        91 bp
        3.1
        SRR22722183_2
        3.3%
        49%
        91 bp
        3.1
        SRR22722184_1
        3.5%
        47%
        91 bp
        3.2
        SRR22722184_2
        3.5%
        47%
        91 bp
        3.2
        SRR22722185_1
        1.9%
        47%
        91 bp
        3.3
        SRR22722185_2
        1.8%
        47%
        91 bp
        3.3
        SRR22722186_1
        1.2%
        51%
        91 bp
        3.2
        SRR22722186_2
        1.2%
        51%
        91 bp
        3.2
        SRR22722187_1
        1.2%
        51%
        91 bp
        3.2
        SRR22722187_2
        1.2%
        51%
        91 bp
        3.2
        SRR24042716_1
        18.7%
        65%
        122 bp
        23.8
        SRR24042716_2
        17.7%
        65%
        122 bp
        23.8
        SRR24042717_1
        14.6%
        64%
        122 bp
        18.3
        SRR24042717_2
        13.8%
        64%
        122 bp
        18.3
        SRR24042718_1
        17.4%
        64%
        122 bp
        18.3
        SRR24042718_2
        16.9%
        64%
        122 bp
        18.3
        SRR24042719_1
        12.7%
        64%
        122 bp
        51.6
        SRR24042719_2
        12.1%
        64%
        122 bp
        51.6
        SRR24042720_1
        9.3%
        63%
        122 bp
        19.9
        SRR24042720_2
        9.9%
        63%
        122 bp
        19.9
        SRR24042721_1
        10.6%
        64%
        122 bp
        24.4
        SRR24042721_2
        10.8%
        64%
        122 bp
        24.4
        SRR24042722_1
        10.8%
        65%
        122 bp
        30.7
        SRR24042722_2
        10.0%
        66%
        122 bp
        30.7
        SRR24042723_1
        8.9%
        60%
        122 bp
        0.6
        SRR24042723_2
        7.7%
        60%
        122 bp
        0.6
        SRR24042724_1
        24.6%
        66%
        122 bp
        24.7
        SRR24042724_2
        23.8%
        66%
        122 bp
        24.7
        SRR24042725_1
        16.2%
        65%
        122 bp
        29.2
        SRR24042725_2
        17.8%
        65%
        122 bp
        29.2
        SRR24042726_1
        12.8%
        65%
        122 bp
        22.3
        SRR24042726_2
        12.5%
        65%
        122 bp
        22.3
        SRR24042727_1
        9.9%
        63%
        122 bp
        23.9
        SRR24042727_2
        9.0%
        63%
        122 bp
        23.9
        SRR24042728_1
        12.7%
        62%
        122 bp
        19.2
        SRR24042728_2
        11.2%
        62%
        122 bp
        19.2
        SRR24042729_1
        8.3%
        61%
        122 bp
        20.6
        SRR24042729_2
        8.2%
        61%
        122 bp
        20.6
        SRR24042730_1
        17.5%
        60%
        122 bp
        19.5
        SRR24042730_2
        17.0%
        61%
        122 bp
        19.5
        SRR24042731_1
        14.9%
        62%
        122 bp
        15.1
        SRR24042731_2
        13.3%
        62%
        122 bp
        15.1
        SRR24042732_1
        25.3%
        64%
        122 bp
        26.1
        SRR24042732_2
        23.8%
        64%
        122 bp
        26.1
        SRR24042733_1
        37.1%
        66%
        122 bp
        16.7
        SRR24042733_2
        35.7%
        66%
        122 bp
        16.7
        SRR24042734_1
        9.8%
        56%
        122 bp
        17.4
        SRR24042734_2
        9.0%
        56%
        122 bp
        17.4
        SRR24042735_1
        10.8%
        65%
        122 bp
        30.6
        SRR24042735_2
        10.7%
        65%
        122 bp
        30.6
        SRR24958367_1
        23.1%
        53%
        132 bp
        15.1
        SRR24958367_2
        22.8%
        53%
        132 bp
        15.1
        SRR24958368_1
        43.5%
        44%
        132 bp
        18.5
        SRR24958368_2
        43.2%
        44%
        132 bp
        18.5
        SRR24958369_1
        53.3%
        57%
        132 bp
        18.6
        SRR24958369_2
        50.1%
        58%
        132 bp
        18.6
        SRR24958430_1
        12.2%
        64%
        132 bp
        17.5
        SRR24958430_2
        12.3%
        64%
        132 bp
        17.5
        SRR24958431_1
        47.9%
        42%
        132 bp
        16.8
        SRR24958431_2
        47.8%
        42%
        132 bp
        16.8
        SRR24958432_1
        7.3%
        63%
        132 bp
        21.4
        SRR24958432_2
        7.0%
        63%
        132 bp
        21.4
        SRR25014987_1
        7.0%
        52%
        130 bp
        29.7
        SRR25014987_2
        6.9%
        52%
        130 bp
        29.7
        SRR26407685_1
        0.8%
        63%
        226 bp
        5.2
        SRR26407685_2
        0.8%
        64%
        226 bp
        5.2
        SRR26407686_1
        1.1%
        53%
        226 bp
        4.7
        SRR26407686_2
        1.0%
        53%
        226 bp
        4.7
        SRR26407687_1
        3.0%
        55%
        226 bp
        4.5
        SRR26407687_2
        2.9%
        55%
        226 bp
        4.5
        SRR26407688_1
        0.8%
        62%
        226 bp
        4.2
        SRR26407688_2
        0.8%
        62%
        226 bp
        4.2
        SRR26407689_1
        0.6%
        55%
        226 bp
        5.0
        SRR26407689_2
        0.6%
        55%
        226 bp
        5.0
        SRR26407690_1
        0.8%
        54%
        226 bp
        5.2
        SRR26407690_2
        0.8%
        54%
        226 bp
        5.2
        SRR26407691_1
        0.7%
        54%
        226 bp
        4.8
        SRR26407691_2
        0.7%
        54%
        226 bp
        4.8
        SRR26407692_1
        1.1%
        63%
        226 bp
        4.7
        SRR26407692_2
        1.1%
        63%
        226 bp
        4.7
        SRR26407693_1
        0.8%
        64%
        226 bp
        5.4
        SRR26407693_2
        0.8%
        64%
        226 bp
        5.4
        SRR27067690_1
        18.9%
        63%
        122 bp
        6.7
        SRR27067690_2
        17.6%
        63%
        122 bp
        6.7
        SRR27067691_1
        1.6%
        66%
        122 bp
        33.7
        SRR27067691_2
        1.5%
        66%
        122 bp
        33.7
        SRR27067692_1
        39.7%
        66%
        122 bp
        8.6
        SRR27067692_2
        37.6%
        66%
        122 bp
        8.6
        SRR27067693_1
        3.8%
        65%
        122 bp
        3.3
        SRR27067693_2
        3.0%
        65%
        122 bp
        3.3
        SRR27067694_1
        11.2%
        65%
        122 bp
        2.1
        SRR27067694_2
        10.3%
        65%
        122 bp
        2.1
        SRR27067695_1
        1.3%
        64%
        122 bp
        4.7
        SRR27067695_2
        1.1%
        64%
        122 bp
        4.7
        SRR27067696_1
        0.9%
        65%
        122 bp
        1.7
        SRR27067696_2
        0.8%
        65%
        122 bp
        1.7
        SRR27067697_1
        14.9%
        65%
        122 bp
        3.8
        SRR27067697_2
        13.6%
        65%
        122 bp
        3.8
        SRR27067698_1
        7.8%
        65%
        122 bp
        2.1
        SRR27067698_2
        7.1%
        65%
        122 bp
        2.1
        SRR27067700_1
        27.6%
        46%
        122 bp
        1.9
        SRR27067700_2
        25.4%
        46%
        122 bp
        1.9
        SRR27067701_1
        22.7%
        66%
        122 bp
        6.2
        SRR27067701_2
        21.1%
        66%
        122 bp
        6.2
        SRR27067702_1
        1.6%
        65%
        122 bp
        30.4
        SRR27067702_2
        1.6%
        65%
        122 bp
        30.4
        SRR27067703_1
        18.6%
        64%
        122 bp
        6.4
        SRR27067703_2
        17.0%
        64%
        122 bp
        6.4
        SRR27067704_1
        1.4%
        59%
        122 bp
        4.5
        SRR27067704_2
        1.2%
        59%
        122 bp
        4.5
        SRR27067705_1
        1.1%
        60%
        122 bp
        6.1
        SRR27067705_2
        1.0%
        60%
        122 bp
        6.1
        SRR27067706_1
        1.3%
        60%
        122 bp
        4.6
        SRR27067706_2
        1.2%
        60%
        122 bp
        4.6
        SRR27067707_1
        5.6%
        64%
        122 bp
        23.4
        SRR27067707_2
        5.2%
        64%
        122 bp
        23.4
        SRR27067708_1
        3.3%
        64%
        116 bp
        34.3
        SRR27067708_2
        3.2%
        64%
        116 bp
        34.3
        SRR27067709_1
        8.3%
        65%
        120 bp
        45.7
        SRR27067709_2
        7.7%
        65%
        120 bp
        45.7
        SRR27067710_1
        6.8%
        63%
        120 bp
        33.5
        SRR27067710_2
        6.3%
        63%
        120 bp
        33.5
        SRR27067711_1
        14.4%
        65%
        120 bp
        65.9
        SRR27067711_2
        13.7%
        65%
        120 bp
        65.9
        SRR27067712_1
        5.5%
        62%
        120 bp
        57.6
        SRR27067712_2
        5.1%
        62%
        120 bp
        57.6
        SRR27067713_1
        2.0%
        64%
        122 bp
        34.5
        SRR27067713_2
        2.0%
        64%
        122 bp
        34.5
        SRR27067714_1
        5.7%
        62%
        122 bp
        39.2
        SRR27067714_2
        5.3%
        62%
        122 bp
        39.2
        SRR27067715_1
        3.2%
        62%
        120 bp
        50.6
        SRR27067715_2
        3.2%
        62%
        120 bp
        50.6
        SRR27067716_1
        2.1%
        60%
        122 bp
        18.9
        SRR27067716_2
        2.0%
        60%
        122 bp
        18.9
        SRR27067718_1
        8.6%
        60%
        122 bp
        3.2
        SRR27067718_2
        7.9%
        60%
        122 bp
        3.2
        SRR27067719_1
        4.1%
        62%
        122 bp
        8.2
        SRR27067719_2
        3.7%
        62%
        122 bp
        8.2
        SRR27067720_1
        4.2%
        61%
        122 bp
        7.9
        SRR27067720_2
        3.8%
        61%
        122 bp
        7.9
        SRR27067721_1
        39.0%
        65%
        120 bp
        7.3
        SRR27067721_2
        37.2%
        66%
        120 bp
        7.3
        SRR27067722_1
        2.9%
        60%
        122 bp
        4.6
        SRR27067722_2
        3.4%
        60%
        122 bp
        4.6
        SRR27067723_1
        6.8%
        63%
        122 bp
        5.2
        SRR27067723_2
        6.3%
        63%
        122 bp
        5.2
        SRR27067724_1
        20.6%
        65%
        122 bp
        6.6
        SRR27067724_2
        19.4%
        65%
        122 bp
        6.6
        SRR27067725_1
        4.4%
        60%
        122 bp
        4.7
        SRR27067725_2
        4.1%
        60%
        122 bp
        4.7
        SRR27067726_1
        19.6%
        63%
        122 bp
        7.5
        SRR27067726_2
        18.7%
        64%
        122 bp
        7.5
        SRR27067727_1
        6.1%
        62%
        122 bp
        6.6
        SRR27067727_2
        5.9%
        62%
        122 bp
        6.6
        SRR27067728_1
        27.7%
        65%
        122 bp
        7.5
        SRR27067728_2
        26.1%
        65%
        122 bp
        7.5
        SRR27067729_1
        1.4%
        62%
        122 bp
        5.8
        SRR27067729_2
        1.3%
        62%
        122 bp
        5.8
        SRR27067730_1
        18.9%
        62%
        122 bp
        6.2
        SRR27067730_2
        18.0%
        62%
        122 bp
        6.2
        SRR27067731_1
        24.5%
        65%
        122 bp
        5.5
        SRR27067731_2
        23.1%
        65%
        122 bp
        5.5
        SRR27067732_1
        2.7%
        62%
        122 bp
        7.4
        SRR27067732_2
        2.5%
        62%
        122 bp
        7.4
        SRR27067733_1
        2.6%
        66%
        122 bp
        28.9
        SRR27067733_2
        2.5%
        66%
        122 bp
        28.9
        SRR27067734_1
        3.7%
        65%
        122 bp
        7.8
        SRR27067734_2
        3.4%
        65%
        122 bp
        7.8
        SRR27067735_1
        2.0%
        62%
        122 bp
        6.8
        SRR27067735_2
        1.8%
        62%
        122 bp
        6.8
        SRR27067736_1
        4.9%
        62%
        122 bp
        28.1
        SRR27067736_2
        4.5%
        62%
        122 bp
        28.1
        SRR27067737_1
        3.2%
        62%
        122 bp
        27.7
        SRR27067737_2
        2.9%
        62%
        122 bp
        27.7
        SRR27067738_1
        3.0%
        62%
        122 bp
        28.4
        SRR27067738_2
        2.7%
        62%
        122 bp
        28.4
        SRR27067739_1
        3.4%
        62%
        122 bp
        27.8
        SRR27067739_2
        3.2%
        62%
        122 bp
        27.8
        SRR27067740_1
        3.0%
        62%
        122 bp
        32.6
        SRR27067740_2
        2.8%
        62%
        122 bp
        32.6
        SRR27067743_1
        6.0%
        61%
        122 bp
        6.2
        SRR27067743_2
        5.7%
        61%
        122 bp
        6.2
        SRR27067744_1
        4.2%
        66%
        122 bp
        30.1
        SRR27067744_2
        4.1%
        66%
        122 bp
        30.1
        SRR27067745_1
        17.5%
        62%
        122 bp
        5.6
        SRR27067745_2
        16.9%
        62%
        122 bp
        5.6
        SRR27067746_1
        9.2%
        60%
        122 bp
        6.4
        SRR27067746_2
        8.2%
        60%
        122 bp
        6.4
        SRR27067747_1
        0.8%
        64%
        122 bp
        4.4
        SRR27067747_2
        1.5%
        64%
        122 bp
        4.4
        SRR27067748_1
        4.7%
        65%
        122 bp
        6.2
        SRR27067748_2
        5.2%
        65%
        122 bp
        6.2
        SRR27067749_1
        1.2%
        64%
        122 bp
        5.7
        SRR27067749_2
        2.0%
        64%
        122 bp
        5.7
        SRR27067750_1
        4.1%
        64%
        122 bp
        6.1
        SRR27067750_2
        6.1%
        64%
        122 bp
        6.1
        SRR27067751_1
        0.8%
        63%
        122 bp
        6.3
        SRR27067751_2
        1.0%
        63%
        122 bp
        6.3
        SRR27067752_1
        0.8%
        64%
        122 bp
        4.1
        SRR27067752_2
        1.5%
        63%
        122 bp
        4.1
        SRR27067753_1
        3.3%
        63%
        122 bp
        4.1
        SRR27067753_2
        4.6%
        63%
        122 bp
        4.1
        SRR27067754_1
        19.0%
        66%
        122 bp
        6.5
        SRR27067754_2
        21.3%
        66%
        122 bp
        6.5
        SRR27067755_1
        1.5%
        66%
        122 bp
        34.2
        SRR27067755_2
        1.4%
        66%
        122 bp
        34.2
        SRR27067756_1
        29.4%
        67%
        122 bp
        6.4
        SRR27067756_2
        28.7%
        67%
        122 bp
        6.4
        SRR27067759_1
        2.8%
        60%
        122 bp
        9.2
        SRR27067759_2
        3.5%
        59%
        122 bp
        9.2
        SRR27067760_1
        4.9%
        62%
        122 bp
        9.6
        SRR27067760_2
        5.8%
        62%
        122 bp
        9.6
        SRR27067761_1
        1.5%
        61%
        122 bp
        8.8
        SRR27067761_2
        1.8%
        61%
        122 bp
        8.8
        SRR27067762_1
        14.6%
        67%
        122 bp
        9.7
        SRR27067762_2
        15.8%
        67%
        122 bp
        9.7
        SRR27067763_1
        1.3%
        64%
        122 bp
        9.5
        SRR27067763_2
        1.6%
        64%
        122 bp
        9.5
        SRR27067764_1
        2.6%
        63%
        122 bp
        9.1
        SRR27067764_2
        2.9%
        63%
        122 bp
        9.1
        SRR27067765_1
        3.6%
        66%
        122 bp
        5.9
        SRR27067765_2
        4.4%
        66%
        122 bp
        5.9
        SRR27067766_1
        3.3%
        66%
        122 bp
        30.5
        SRR27067766_2
        3.2%
        66%
        122 bp
        30.5
        SRR27067767_1
        1.4%
        62%
        122 bp
        5.8
        SRR27067767_2
        1.8%
        62%
        122 bp
        5.8
        SRR27067768_1
        3.0%
        64%
        122 bp
        6.9
        SRR27067768_2
        3.6%
        64%
        122 bp
        6.9
        SRR27067769_1
        2.6%
        64%
        122 bp
        7.3
        SRR27067769_2
        2.6%
        64%
        122 bp
        7.3
        SRR27067770_1
        2.4%
        63%
        122 bp
        7.6
        SRR27067770_2
        2.7%
        63%
        122 bp
        7.6
        SRR27067772_1
        18.3%
        67%
        122 bp
        24.7
        SRR27067772_2
        19.5%
        67%
        122 bp
        24.7
        SRR27067773_1
        21.7%
        66%
        122 bp
        30.6
        SRR27067773_2
        21.3%
        66%
        122 bp
        30.6
        SRR27067774_1
        15.8%
        64%
        122 bp
        28.1
        SRR27067774_2
        15.5%
        64%
        122 bp
        28.1
        SRR27067775_1
        6.4%
        64%
        122 bp
        29.6
        SRR27067775_2
        6.3%
        64%
        122 bp
        29.6
        SRR27067776_1
        5.1%
        63%
        122 bp
        32.7
        SRR27067776_2
        5.0%
        63%
        122 bp
        32.7
        SRR27067777_1
        0.9%
        65%
        122 bp
        8.8
        SRR27067777_2
        0.8%
        65%
        122 bp
        8.8
        SRR27067778_1
        4.8%
        63%
        122 bp
        26.7
        SRR27067778_2
        4.4%
        64%
        122 bp
        26.7
        SRR27067779_1
        6.2%
        67%
        122 bp
        31.2
        SRR27067779_2
        6.0%
        67%
        122 bp
        31.2
        SRR27067780_1
        16.0%
        67%
        122 bp
        29.3
        SRR27067780_2
        15.4%
        67%
        122 bp
        29.3
        SRR27067781_1
        14.0%
        65%
        122 bp
        31.6
        SRR27067781_2
        14.5%
        65%
        122 bp
        31.6
        SRR27067782_1
        0.8%
        65%
        122 bp
        7.3
        SRR27067782_2
        0.7%
        65%
        122 bp
        7.3
        SRR27067783_1
        0.8%
        65%
        122 bp
        8.0
        SRR27067783_2
        0.8%
        65%
        122 bp
        8.0
        SRR27067784_1
        0.8%
        65%
        122 bp
        6.9
        SRR27067784_2
        0.8%
        65%
        122 bp
        6.9
        SRR27067786_1
        1.3%
        65%
        122 bp
        32.9
        SRR27067786_2
        1.3%
        65%
        122 bp
        32.9
        SRR27067788_1
        1.2%
        63%
        122 bp
        13.3
        SRR27067788_2
        1.1%
        63%
        122 bp
        13.3
        SRR27067789_1
        7.5%
        64%
        122 bp
        5.8
        SRR27067789_2
        7.0%
        65%
        122 bp
        5.8
        SRR27067790_1
        1.3%
        62%
        116 bp
        6.2
        SRR27067790_2
        1.2%
        62%
        116 bp
        6.2
        SRR27067791_1
        4.2%
        54%
        122 bp
        6.8
        SRR27067791_2
        4.0%
        55%
        122 bp
        6.8
        SRR27067792_1
        4.6%
        67%
        122 bp
        35.0
        SRR27067792_2
        4.6%
        67%
        122 bp
        35.0
        SRR27067793_1
        0.9%
        66%
        122 bp
        6.9
        SRR27067793_2
        0.9%
        66%
        122 bp
        6.9
        SRR27067794_1
        1.2%
        64%
        122 bp
        8.9
        SRR27067794_2
        1.1%
        64%
        122 bp
        8.9
        SRR27205360_1
        2.3%
        42%
        140 bp
        26.5
        SRR27205360_2
        2.3%
        42%
        140 bp
        26.5
        SRR27205362_1
        2.8%
        42%
        140 bp
        58.7
        SRR27205362_2
        2.7%
        42%
        140 bp
        58.7
        SRR27205363_1
        4.2%
        43%
        140 bp
        26.7
        SRR27205363_2
        4.0%
        43%
        140 bp
        26.7
        SRR27205364_1
        6.1%
        43%
        140 bp
        61.2
        SRR27205364_2
        5.6%
        43%
        140 bp
        61.2
        SRR27205365_1
        2.8%
        45%
        140 bp
        28.4
        SRR27205365_2
        2.7%
        45%
        140 bp
        28.4
        SRR27205366_1
        3.6%
        45%
        140 bp
        60.4
        SRR27205366_2
        3.5%
        45%
        140 bp
        60.4
        SRR27205367_1
        2.9%
        47%
        140 bp
        46.1
        SRR27205367_2
        2.4%
        47%
        140 bp
        46.1
        SRR27205368_1
        2.4%
        47%
        140 bp
        44.9
        SRR27205368_2
        2.1%
        47%
        140 bp
        44.9
        SRR27205369_1
        26.5%
        38%
        140 bp
        15.0
        SRR27205369_2
        25.5%
        38%
        140 bp
        15.0
        SRR27205370_1
        17.0%
        54%
        140 bp
        63.4
        SRR27205370_2
        15.5%
        55%
        140 bp
        63.4
        SRR27205373_1
        45.2%
        38%
        140 bp
        65.4
        SRR27205373_2
        43.9%
        38%
        140 bp
        65.4
        SRR27205378_1
        8.4%
        55%
        140 bp
        19.9
        SRR27205378_2
        7.6%
        55%
        140 bp
        19.9
        SRR28178500_1
        37.0%
        66%
        140 bp
        37.3
        SRR28178500_2
        36.1%
        66%
        140 bp
        37.3
        SRR28275267_1
        8.9%
        57%
        132 bp
        28.9
        SRR28275267_2
        8.7%
        57%
        132 bp
        28.9
        SRR28275268_1
        8.4%
        61%
        132 bp
        18.3
        SRR28275268_2
        8.3%
        61%
        132 bp
        18.3
        SRR28275269_1
        5.3%
        57%
        132 bp
        23.3
        SRR28275269_2
        5.1%
        57%
        132 bp
        23.3
        SRR28926225_1
        1.7%
        60%
        114 bp
        7.1
        SRR28926225_2
        1.7%
        60%
        120 bp
        7.1
        SRR28958689_1
        4.2%
        62%
        124 bp
        7.6
        SRR28958689_2
        4.1%
        62%
        124 bp
        7.6
        SRR30312859_1
        9.2%
        61%
        130 bp
        25.3
        SRR30312859_2
        7.6%
        61%
        130 bp
        25.3
        SRR30312860_1
        4.6%
        62%
        140 bp
        199.7
        SRR30312860_2
        4.3%
        62%
        140 bp
        199.7
        SRR30650669_1
        61.2%
        53%
        130 bp
        9.7
        SRR30650669_2
        58.9%
        53%
        130 bp
        9.7
        SRR30650670_1
        71.7%
        52%
        130 bp
        15.0
        SRR30650670_2
        69.6%
        52%
        130 bp
        15.0
        SRR30650671_1
        67.3%
        52%
        130 bp
        23.8
        SRR30650671_2
        65.7%
        52%
        130 bp
        23.8
        SRR30650678_1
        73.5%
        57%
        130 bp
        26.0
        SRR30650678_2
        71.7%
        57%
        130 bp
        26.0
        SRR31455428_1
        5.5%
        63%
        130 bp
        2.0
        SRR31455428_2
        5.3%
        63%
        130 bp
        2.0
        SRR33949953_1
        7.0%
        43%
        130 bp
        5.9
        SRR33949953_2
        7.0%
        43%
        130 bp
        5.9
        SRR33949954_1
        4.0%
        56%
        130 bp
        37.9
        SRR33949954_2
        4.0%
        56%
        130 bp
        37.9
        SRR33949955_1
        4.8%
        54%
        130 bp
        39.5
        SRR33949955_2
        4.6%
        54%
        130 bp
        39.5
        SRR33949956_1
        3.1%
        56%
        130 bp
        40.4
        SRR33949956_2
        3.0%
        56%
        130 bp
        40.4
        SRR33949957_1
        3.3%
        57%
        130 bp
        41.2
        SRR33949957_2
        3.2%
        57%
        130 bp
        41.2
        SRR33949958_1
        3.8%
        57%
        130 bp
        37.3
        SRR33949958_2
        3.8%
        57%
        130 bp
        37.3
        SRR33949959_1
        3.9%
        57%
        130 bp
        43.4
        SRR33949959_2
        3.8%
        57%
        130 bp
        43.4
        SRR33949960_1
        4.7%
        55%
        130 bp
        50.7
        SRR33949960_2
        4.6%
        55%
        130 bp
        50.7
        SRR33949962_1
        18.3%
        40%
        130 bp
        37.0
        SRR33949962_2
        18.4%
        40%
        130 bp
        37.0
        SRR33949963_1
        18.8%
        52%
        130 bp
        42.8
        SRR33949963_2
        18.8%
        52%
        130 bp
        42.8
        SRR33949964_1
        25.3%
        54%
        130 bp
        38.9
        SRR33949964_2
        25.4%
        54%
        130 bp
        38.9
        SRR7080745_1
        43.2%
        46%
        122 bp
        43.0
        SRR7080745_2
        43.3%
        46%
        122 bp
        43.0
        SRR7741201_1
        5.6%
        55%
        267 bp
        1.0
        SRR7741201_2
        5.0%
        55%
        247 bp
        1.0
        SRR7811943_1
        16.4%
        61%
        132 bp
        79.1
        SRR7811943_2
        16.6%
        61%
        132 bp
        79.1
        SRR7811987_1
        4.5%
        61%
        132 bp
        89.2
        SRR7811987_2
        4.6%
        61%
        132 bp
        89.2
        SRR8536157_1
        12.9%
        57%
        132 bp
        176.4
        SRR8536157_2
        12.8%
        57%
        132 bp
        176.4
        SRR8536158_1
        3.9%
        55%
        132 bp
        6.5
        SRR8536158_2
        3.8%
        55%
        132 bp
        6.5
        SRR8856740_1
        4.9%
        60%
        132 bp
        47.6
        SRR8856740_2
        4.6%
        60%
        132 bp
        47.6
        SRR9599867_1
        0.6%
        59%
        132 bp
        5.8
        SRR9599867_2
        0.5%
        59%
        132 bp
        5.8

        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        482 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 3/3 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAA
        1
        106310
        0.0007%
        GCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGC
        1
        113811
        0.0008%
        ATTGTACTTCAAGGCGGCCAGCGCGGCTCGTCCGCCGCGATGGCTTGGCC
        1
        29698
        0.0002%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1